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What is PatternLab?

PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. PatternLab contains modules for formatting sequence databases, performing peptide spectrum matching, statistically filtering and organizing shotgun proteomic data, extracting quantitative information from label-free and chemically labeled data, performing statistics for differential proteomics, displaying results in a variety of graphical formats, performing similarity-driven studies with de novo sequencing data, and analyzing time-course experiments. Here, we present PatternLab for Proteomics V, which closely knits together all these modules in a self-contained environment, covering the principal aspects of proteomic data analysis as freely available and easily installable software.PatternLab is user-friendly, simple and provides a graphical user interface.

Please cite:

doi> “Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0”, Nature Protocols (11), 102-117, 2016.

What's New?

PatternLab V represents a leap in user experience.

Paulo C. Carvalho Researcher


doi> "PatternLab for proteomics: a tool for differential shotgun proteomics.", BMC bioinformatics, v. 9, p. 316, 2008.

doi> “Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0”, Nature Protocols (11), 102-117, 2016.

doi> “Simple, efficient, and thorough shotgun proteomic analysis with PatternLab for proteomics V” (Submitted)


Example dataset can be download here.
Search Comet - Peptide Spectrum Matching
Filter SEPro - Search Engine Processor
Please refer to our protocol for downstream bioinformatic analysis.


Dalton Mass Spectrometry Lab

UNICAMP - Brazil Group - Leader: Fabio C Gozzo

Toxinology Laboratory

Fiocruz/RJ - Brazil - Group Leader: Ana G C N Ferreira

Proteomics Unit

Chemistry Institute/UFRJ - Brazil - Group Leader: Gilberto B Domont

Hermjakob Group

EMBL/EBI - UK - Bioinformatician: Yasset P Riverol

Yates Laboratory

The Scripps Research Institute - USA - Group Leader: John R Yates III

Analytical Biochemistry and Proteomics Unit

Institut Pasteur - Uruguay - Group Leader: Rosario Durán

Systems Engineering and Computer Science Program

COPPE/UFRJ - Brazil - Group Leader: Valmir C Barbosa

Mass Spectrometry for Biology Unit

Institut Pasteur - Paris - Group Leader: Julia Chamot-Rooke

Department Genome Sciences

University of Washington - USA - Group Leader: Jimmy K. Eng


Mia Donovan

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information.

Mia Donovan

A public repository of protein and peptide identifications for the proteomics community.


Laboratory for Computational and Strucutural Proteomics - Fiocruz
Rua Professor Algacyr Munhoz Mader, 3775
Cidade Industrial - Curitiba - PR
CEP: 81310-020